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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, Tushabe P, Bukenya H, Namuwulya P, Kabaliisa T, Birungi M, Tibanagwa M, Ampeire I, Kakooza P, Katushabe E, Bwogi J, Bakamutumaho B, Nanyunja M, Byabamazima CR. The road to a polio-free Uganda; contribution of the Expanded Program on Immunization Laboratory (EPI-LAB) at Uganda Virus Research Institute. Afr Health Sci 2023; 23:186-196. [PMID: 38357183 PMCID: PMC10862580 DOI: 10.4314/ahs.v23i3.23] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Background The control of poliomyelitis in Uganda dates back as far as 1950 and acute flaccid paralysis (AFP) surveillance has since been used as a criterion for identifying wild polioviruses. Poliovirus isolation was initially pursued through collaborative research however, in 1993, the Expanded Program on Immunization Laboratory (EPI-LAB) was established as a member of the Global Poliovirus Laboratory Network (GPLN) and spearheaded this activity at Uganda Virus Research Institute. Objectives The aim of this report is to document the progress and impact of the EPI-LAB on poliovirus eradication in Uganda. Methods Poliovirus detection and identification were achieved fundamentally through tissue culture and intra-typic differentiation of the poliovirus based on the real-time reverse transcriptase polymerase chain reaction (rRT PCR). The data obtained was entered into the national AFP database and analysed using EpiInfoTM statistical software. Results Quantitative and qualitative detection of wild and Sabin polioviruses corresponded with the polio campaigns. The WHO target indicators for AFP surveillance were achieved essentially throughout the study period. Conclusion Virological tracking coupled with attaining standard AFP surveillance indicators has been pivotal in achieving and maintaining the national wild polio-free status. Laboratory surveillance remains key in informing the certification process of polio eradication.
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Affiliation(s)
- Mary B Nanteza
- 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
| | - Henry Bukenya
- 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
| | - Theopista Kabaliisa
- 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
| | - Mayi Tibanagwa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Immaculate Ampeire
- Ministry of Health, Government of Uganda, Plot 6, Lourdel Road, Nakasero P. O. Box 7272, Kampala, Uganda
| | - Proscovia Kakooza
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Edson Katushabe
- World Health Organization Office, Plot 60 Prince Charles Avenue, Kololo, Kampala
| | - Josephine Bwogi
- 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
| | - Miriam Nanyunja
- World Health Organization AFRO, East and Southern Africa (ESA), Nairobi, 45335 Nairobi, Kenya
| | - Charles R Byabamazima
- World Health Organization AFRO, East and Southern Africa (ESA), Harare, 82-86 Enterprise Road, Highlands, P. O. Box BE 773, Belvedere, Harare, Zimbabwe
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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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5
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Kigozi BK, Kharod GA, Bukenya H, Shadomy SV, Haberling DL, Stoddard RA, Galloway RL, Tushabe P, Nankya A, Nsibambi T, Mbidde EK, Lutwama JJ, Perniciaro JL, Nicholson WL, Bower WA, Bwogi J, Blaney DD. Investigating the etiology of acute febrile illness: a prospective clinic-based study in Uganda. BMC Infect Dis 2023; 23:411. [PMID: 37328808 PMCID: PMC10276394 DOI: 10.1186/s12879-023-08335-4] [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: 12/25/2022] [Accepted: 05/17/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Historically, malaria has been the predominant cause of acute febrile illness (AFI) in sub-Saharan Africa. However, during the last two decades, malaria incidence has declined due to concerted public health control efforts, including the widespread use of rapid diagnostic tests leading to increased recognition of non-malarial AFI etiologies. Our understanding of non-malarial AFI is limited due to lack of laboratory diagnostic capacity. We aimed to determine the etiology of AFI in three distinct regions of Uganda. METHODS A prospective clinic-based study that enrolled participants from April 2011 to January 2013 using standard diagnostic tests. Participant recruitment was from St. Paul's Health Centre (HC) IV, Ndejje HC IV, and Adumi HC IV in the western, central and northern regions, which differ by climate, environment, and population density. A Pearson's chi-square test was used to evaluate categorical variables, while a two-sample t-test and Krukalis-Wallis test were used for continuous variables. RESULTS Of the 1281 participants, 450 (35.1%), 382 (29.8%), and 449 (35.1%) were recruited from the western, central, and northern regions, respectively. The median age (range) was 18 (2-93) years; 717 (56%) of the participants were female. At least one AFI pathogen was identified in 1054 (82.3%) participants; one or more non-malarial AFI pathogens were identified in 894 (69.8%) participants. The non-malarial AFI pathogens identified were chikungunya virus, 716 (55.9%); Spotted Fever Group rickettsia (SFGR), 336 (26.2%) and Typhus Group rickettsia (TGR), 97 (7.6%); typhoid fever (TF), 74 (5.8%); West Nile virus, 7 (0.5%); dengue virus, 10 (0.8%) and leptospirosis, 2 (0.2%) cases. No cases of brucellosis were identified. Malaria was diagnosed either concurrently or alone in 404 (31.5%) and 160 (12.5%) participants, respectively. In 227 (17.7%) participants, no cause of infection was identified. There were statistically significant differences in the occurrence and distribution of TF, TGR and SFGR, with TF and TGR observed more frequently in the western region (p = 0.001; p < 0.001) while SFGR in the northern region (p < 0.001). CONCLUSION Malaria, arboviral infections, and rickettsioses are major causes of AFI in Uganda. Development of a Multiplexed Point-of-Care test would help identify the etiology of non-malarial AFI in regions with high AFI rates.
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Affiliation(s)
- Brian K Kigozi
- Uganda Virus Research Institute, Entebbe, Uganda.
- College of Health Sciences, Clinical Epidemiology Unit, Makerere University, Kampala, Uganda.
| | - Grishma A Kharod
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - Sean V Shadomy
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Dana L Haberling
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Robyn A Stoddard
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Renee L Galloway
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - Annet Nankya
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Thomas Nsibambi
- Uganda Virus Research Institute, Entebbe, Uganda
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | | | | | | | | | - William A Bower
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - David D Blaney
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
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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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Namuwulya P, Bukenya H, Tushabe P, Tweyongyere R, Bwogi J, Cotten M, Phan MVT. Near-Complete Genome Sequences of Measles Virus Strains from 10 Years of Uganda Country-wide Surveillance. Microbiol Resour Announc 2022; 11:e0060622. [PMID: 35876572 PMCID: PMC9387275 DOI: 10.1128/mra.00606-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/08/2022] [Indexed: 11/20/2022] Open
Abstract
Measles remains a global health challenge despite the availability of a safe and effective vaccine. Sporadic outbreaks of measles virus infections continue in Uganda. We report eight near-complete genome sequences of measles virus strains from Uganda cases from 2011 to 2020, providing useful data for assessing vaccine escape and local/regional transmission.
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Affiliation(s)
| | | | | | - Robert Tweyongyere
- Department of Veterinary Pharmacy Clinical and Comparative Medicine, Makerere University, Kampala, Uganda
| | | | - Matthew Cotten
- U.K. Medical Research Council-Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- U.K. Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - My V. T. Phan
- U.K. Medical Research Council-Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
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8
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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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9
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Tushabe P, Howard W, Bwogi J, Birungi M, Eliku JP, Kakooza P, Bukenya H, Namuwulya P, Gaizi J, Tibanagwa M, Kabaliisa T, Mulindwa J, Muhanguzi D, Suchard M, Gumede N, Bakamutumaho B. Molecular characterization of non-polio enteroviruses isolated from acute flaccid paralysis patients in Uganda. J Med Virol 2021; 93:4720-4728. [PMID: 33458840 PMCID: PMC9787851 DOI: 10.1002/jmv.26804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/20/2020] [Revised: 12/18/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022]
Abstract
Enteroviruses (EVs) are RNA viruses that can cause many clinical syndromes including acute flaccid paralysis (AFP). Within the global polio laboratory network, EVs are categorized either as polioviruses or non-polio enteroviruses (NPEVs). Specific NPEVs have been described in polio-like residual paralytic events in AFP patients. Retrospective analysis of 112 NPEV isolates from AFP patients was performed and thirty one NPEV types were identified of which 91% were Enterovirus B and 9% were Enterovirus A species. The NPEVs were distributed across the country with most patients in the eastern region (41/89; 46.1%). The highest proportion of patients were children less than 5 years (77/89; 86.5%) and male patients were more common (54/89; 60.7%). Echovirus 11 (11/89; 12.4%) was frequently observed and phylogenetic analysis of these sequences revealed high diversity. Coxsackievirus B5 (CV-B5), CV-B6, E21, and EV-B69 were only seen in patients with residual paralysis. Analyses of the EV-A71 sequence indicated a unique genogroup.
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Affiliation(s)
| | - Wayne Howard
- National Institute for Communicable DiseasesJohannesburgSouth Africa
| | | | - Molly Birungi
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | - James P. Eliku
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Henry Bukenya
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Joseph Gaizi
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | - Mayi Tibanagwa
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Julius Mulindwa
- Department of Biochemistry and Sports Sciences, College of Natural SciencesSchool of Biological Sciences, Makerere UniversityKampalaUganda
| | - Dennis Muhanguzi
- Department of Biomolecular Resources and Biolaboratory SciencesCollege of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampalaUganda
| | - Melinda Suchard
- National Institute for Communicable DiseasesJohannesburgSouth Africa,University of WitwatersrandJohannesburgSouth Africa
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10
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Tushabe P, Bwogi J, Abernathy E, Birungi M, Eliku JP, Seguya R, Bukenya H, Namuwulya P, Kakooza P, Suppiah S, Kabaliisa T, Tibanagwa M, Ampaire I, Kisakye A, Bakainaga A, Byabamazima CR, Icenogle JP, Bakamutumaho B. Descriptive epidemiology of rubella disease and associated virus strains in Uganda. J Med Virol 2020; 92:279-287. [PMID: 31598987 PMCID: PMC7004003 DOI: 10.1002/jmv.25604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/24/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Abstract
Rubella virus causes a mild disease; however, infection during the first trimester of pregnancy may lead to congenital rubella syndrome (CRS) in over 80% of affected pregnancies. Vaccination is recommended and has been shown to effectively reduce CRS incidence. Uganda plans to introduce routine rubella vaccination in 2019. The World Health Organization recommends assessing the disease burden and obtaining the baseline molecular virological data before vaccine introduction. Sera collected during case-based measles surveillance from January 2005 to July 2018 were tested for rubella immunoglobulin M (IgM) antibodies. Sera from confirmed rubella outbreaks from January 2012 to August 2017 were screened using real-time reverse-transcription polymerase chain reaction (RT-PCR); for positive samples, a region within the E1 glycoprotein coding region was amplified and sequenced. Of the 23 196 suspected measles cases serologically tested in parallel for measles and rubella, 5334 (23%) were rubella IgM-positive of which 2710 (50.8%) cases were females with 2609 (96.3%) below 15 years of age. Rubella IgM-positive cases were distributed throughout the country and the highest number was detected in April, August, and November. Eighteen (18%) of the 100 sera screened were real-time RT-PCR-positive of which eight (44.4%) were successfully sequenced and genotypes 1G and 2B were identified. This study reports on the seroprevalence and molecular epidemiology of rubella. Increased knowledge of former and current rubella viruses circulating in Uganda will enhance efforts to monitor the impact of vaccination as Uganda moves toward control and elimination of rubella and CRS.
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Affiliation(s)
| | | | - Emily Abernathy
- Division of Viral Diseases, National Center for Immunization and Respiratory DiseasesUnited States Centers for Disease Control and PreventionAtlantaGeorgia
| | - Molly Birungi
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | - James P. Eliku
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Henry Bukenya
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | | | - Suganthi Suppiah
- Division of Viral Diseases, National Center for Immunization and Respiratory DiseasesUnited States Centers for Disease Control and PreventionAtlantaGeorgia
| | | | - Mayi Tibanagwa
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | | | | | - Charles R. Byabamazima
- WHO Inter‐Country Support Team Office For Eastern and Southern Africa (IST/ESA)HarareZimbabwe
| | - Joseph P. Icenogle
- Division of Viral Diseases, National Center for Immunization and Respiratory DiseasesUnited States Centers for Disease Control and PreventionAtlantaGeorgia
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11
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Nanteza MB, Bakamutumaho B, Kisakye A, Namuwulya P, Bukenya H, Katushabe E, Bwogi J, Byabamazima CR, Williams R, Gumede N. The detection of 3 ambiguous type 2 vaccine-derived polioviruses (VDPV2s) in Uganda. Virol J 2018; 15:77. [PMID: 29699577 PMCID: PMC5922010 DOI: 10.1186/s12985-018-0990-y] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Oral Polio Vaccine (OPV or Sabin) is genetically unstable and may mutate to form vaccine-derived polioviruses (VDPVs). METHODS In 2014, two VDPVs type 2 were identified during routine surveillance of acute flaccid paralysis (AFP) cases. Consequently, a retrospective VDPV survey was conducted to ensure that there was no circulating VDPV in the country. All Sabin poliovirus isolates identified in Uganda 6 months before and 6 months after were re-screened; Sabin 1 and 3 polioviruses were re-screened for Sabin 2 and Sabin 2 polioviruses were re-screened for VDPVs type 2. The Poliovirus rRT-PCR ITD/VDPV 4.0 assay and sequencing were used respectively. RESULTS The first two VDPVs type2 were identified in Eastern Uganda and the third was identified during the survey from South-western Uganda. These regions had low OPV coverage and poor AFP surveillance indicators. CONCLUSION The retrospective VDPV survey was a useful strategy to screen for VDPVs more exhaustively. Supplementary surveillance methods need to be encouraged.
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Affiliation(s)
- Mary Bridget Nanteza
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda.
| | - Barnabas Bakamutumaho
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Annet Kisakye
- World Health Organization (WHO), Plot 60 Prince Charles Avenue, Kololo, P.O. Box 24578, Kampala, Uganda
| | - Prossy Namuwulya
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Edson Katushabe
- World Health Organization (WHO), Plot 60 Prince Charles Avenue, Kololo, P.O. Box 24578, Kampala, Uganda
| | - Josephine Bwogi
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | | | - Raffaella Williams
- National Institute for Communicable Diseases (NICD), 1 Modderfontein Road Sandringham Johannesburg. Private Bag x4, Sandringham, 2131, South Africa.,NSW HIV State Reference Laboratory, St Vicent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Nicksy Gumede
- World Health Organization, Regional Office for Africa, P.O. Box 06, Brazzaville, Republic of Congo
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12
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Kharod G, haberling D, Person M, Folkema A, Galloway R, Elrod M, Perniciaro J, Nicholson W, Patel N, Bwogi J, Bukenya H, Drakeley C, Mbulaiteye S, Blaney D, Shadomy S. Uganda National Acute Febrile Illness Agent Detection Serosurvey 2004-2005. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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13
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Namuwulya P, Abernathy E, Bukenya H, Bwogi J, Tushabe P, Birungi M, Seguya R, Kabaliisa T, Alibu VP, Kayondo JK, Rivailler P, Icenogle J, Bakamutumaho B. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012. J Med Virol 2014; 86:2107-13. [PMID: 24700073 DOI: 10.1002/jmv.23935] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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] [Accepted: 02/27/2014] [Indexed: 11/07/2022]
Abstract
Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.
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14
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Kizito D, Tweyongyere R, Namatovu A, Webb EL, Muhangi L, Lule SA, Bukenya H, Cose S, Elliott AM. Factors affecting the infant antibody response to measles immunisation in Entebbe-Uganda. BMC Public Health 2013; 13:619. [PMID: 23816281 PMCID: PMC3733798 DOI: 10.1186/1471-2458-13-619] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 06/25/2013] [Indexed: 11/24/2022] Open
Abstract
Background Vaccine failure is an important concern in the tropics with many contributing elements. Among them, it has been suggested that exposure to natural infections might contribute to vaccine failure and recurrent disease outbreaks. We tested this hypothesis by examining the influence of co-infections on maternal and infant measles-specific IgG levels. Methods We conducted an observational analysis using samples and data that had been collected during a larger randomised controlled trial, the Entebbe Mother and Baby Study (ISRCTN32849447). For the present study, 711 pregnant women and their offspring were considered. Helminth infections including hookworm, Schistosoma mansoni and Mansonella perstans, along with HIV, malaria, and other potential confounding factors were determined in mothers during pregnancy and in their infants at age one year. Infants received their measles immunisation at age nine months. Levels of total IgG against measles were measured in mothers during pregnancy and at delivery, as well as in cord blood and from infants at age one year. Results Among the 711 pregnant women studied, 66% had at least one helminth infection at enrolment, 41% had hookworm, 20% M. perstans and 19% S. mansoni. Asymptomatic malaria and HIV prevalence was 8% and 10% respectively. At enrolment, 96% of the women had measles-specific IgG levels considered protective (median 4274 mIU/ml (IQR 1784, 7767)). IgG levels in cord blood were positively correlated to maternal measles-specific IgG levels at delivery (r = 0.81, p < 0.0001). Among the infants at one year of age, median measles-specific IgG levels were markedly lower than in maternal and cord blood (median 370 mIU/ml (IQR 198, 656) p < 0.0001). In addition, only 75% of the infants had measles-specific IgG levels considered to be protective. In a multivariate regression analysis, factors associated with reduced measles-specific antibody levels in infancy were maternal malaria infection, infant malaria parasitaemia, infant HIV and infant wasting. There was no association with maternal helminth infection. Conclusion Malaria and HIV infection in mothers during pregnancy, and in their infants, along with infant malnutrition, may result in reduction of the antibody response to measles immunisation in infancy. This re-emphasises the importance of malaria and HIV control, and support for infant nutrition, as these interventions may have benefits for vaccine efficacy in tropical settings.
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Affiliation(s)
- Dennison Kizito
- Co-infection Studies Programme, MRC/UVRI Uganda Research Unit on AIDS, Uganda Virus Research Institute, PO BOX 49, Entebbe, Uganda.
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15
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Rota PA, Brown K, Mankertz A, Santibanez S, Shulga S, Muller CP, Hübschen JM, Siqueira M, Beirnes J, Ahmed H, Triki H, Al-Busaidy S, Dosseh A, Byabamazima C, Smit S, Akoua-Koffi C, Bwogi J, Bukenya H, Wairagkar N, Ramamurty N, Incomserb P, Pattamadilok S, Jee Y, Lim W, Xu W, Komase K, Takeda M, Tran T, Castillo-Solorzano C, Chenoweth P, Brown D, Mulders MN, Bellini WJ, Featherstone D. Global Distribution of Measles Genotypes and Measles Molecular Epidemiology. J Infect Dis 2011; 204 Suppl 1:S514-23. [DOI: 10.1093/infdis/jir118] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Baliraine FN, Bwogi J, Bukenya H, Seguya R, Kabaliisa T, Kisakye A, Mbabazi WB, Smit SB. Possible interruption of measles virus transmission, Uganda, 2006-2009. Emerg Infect Dis 2011; 17:110-3. [PMID: 21192868 PMCID: PMC3204633 DOI: 10.3201/eid1701.100753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To determine what measles virus genotype(s) circulated in Uganda after strategic interventions aimed at controlling/eliminating measles, we examined samples obtained during 2006-2009 and found only genotype B3.1, which had not been previously detected. Kenya was the likely source, but other countries cannot be excluded.
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Affiliation(s)
- Frederick N Baliraine
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94143-0811, USA.
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Rota J, Lowe L, Rota P, Bellini W, Redd S, Dayan G, van Binnendijk R, Hahné S, Tipples G, Macey J, Espinoza R, Posey D, Plummer A, Bateman J, Gudiño J, Cruz-Ramirez E, Lopez-Martinez I, Anaya-Lopez L, Holy Akwar T, Giffin S, Carrión V, de Filippis AMB, Vicari A, Tan C, Wolf B, Wytovich K, Borus P, Mbugua F, Chege P, Kombich J, Akoua-Koffi C, Smit S, Bukenya H, Bwogi J, Baliraine FN, Kremer J, Muller C, Santibanez S. Identical genotype B3 sequences from measles patients in 4 countries, 2005. Emerg Infect Dis 2007; 12:1779-81. [PMID: 17283637 PMCID: PMC3372353 DOI: 10.3201/eid1211.060635] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Surveillance of measles virus detected an epidemiologic link between a refugee from Kenya and a Dutch tourist in New Jersey, USA. Identical genotype B3 sequences from patients with contemporaneous cases in the United States, Canada, and Mexico in November and December 2005 indicate that Kenya was likely to have been the common source of virus.
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Affiliation(s)
- Jennifer Rota
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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