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  1. Article ; Online: Implementing SARS-CoV-2 antigen testing scale-up in Rwanda: retrospective analysis of national programme data and qualitative findings.

    Rutayisire, Robert / Boeke, Caroline E / Joseph, Jessica / Bansal, Namita / Bigirimana, Noella / Demke, Owen / Kallarakal, Ashley / Karame, Prosper / Ndayishimiye, Rodrigue / Umumararungu, Esperance / Peter, Trevor / Khan, Shaukat

    BMJ open

    2023  Volume 13, Issue 4, Page(s) e066776

    Abstract: Objectives: Reverse transcriptase PCR is the most sensitive test for SARS-CoV-2 diagnosis. However, the scale-up of these tests in low-income and middle-income countries (LMICs) has been limited due to infrastructure and cost. Antigen rapid diagnostic ... ...

    Abstract Objectives: Reverse transcriptase PCR is the most sensitive test for SARS-CoV-2 diagnosis. However, the scale-up of these tests in low-income and middle-income countries (LMICs) has been limited due to infrastructure and cost. Antigen rapid diagnostic tests are an alternative option for diagnosing active infection that may allow for faster, easier, less expensive and more widespread testing. We compared the implementation of antigen and PCR testing programmes in Rwanda.
    Design: We retrospectively reviewed routinely collected PCR and antigen testing data for all reported tests conducted nationally. We administered semiquantitative surveys to healthcare workers (HCWs) involved in COVID-19 testing and care and clients receiving antigen testing.
    Setting: Rwanda, November 2020-July 2021.
    Participants: National SARS-CoV-2 testing data; 49 HCWs involved in COVID-19 testing and care; 145 clients receiving antigen testing.
    Interventions: None (retrospective analysis of programme data).
    Primary and secondary outcome measures: Test volumes, turnaround times, feasibility and acceptability of antigen testing.
    Results: Data from 906 204 antigen tests and 445 235 PCR tests were included. Antigen testing increased test availability and case identification compared with PCR and had a median results return time of 0 days (IQR: 0-0). In contrast, PCR testing time ranged from 1 to 18 days depending on the sample collection site/district. Both HCWs and clients indicated that antigen testing was feasible and acceptable. Some HCWs identified stockouts and limited healthcare staff as challenges.
    Conclusions: Antigen testing facilitated rapid expansion and decentralisation of SARS-CoV-2 testing across lower tier facilities in Rwanda, contributed to increased case identification, reduced test processing times, and was determined to be feasible and acceptable to clients and providers. Antigen testing will be an essential component of SARS-CoV-2 test and treat programmes in LMICs.
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19/diagnosis ; COVID-19 Testing ; Retrospective Studies ; COVID-19 Serological Testing ; Rwanda
    Language English
    Publishing date 2023-04-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2599832-8
    ISSN 2044-6055 ; 2044-6055
    ISSN (online) 2044-6055
    ISSN 2044-6055
    DOI 10.1136/bmjopen-2022-066776
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Prevalence of Hepatitis C Virus Infection and Its Risk Factors among Patients Attending Rwanda Military Hospital, Rwanda.

    Umumararungu, Esperance / Ntaganda, Fabien / Kagira, John / Maina, Naomi

    BioMed research international

    2017  Volume 2017, Page(s) 5841272

    Abstract: In Rwanda, the prevalence of viral hepatitis (HCV) is poorly understood. The current study investigated the prevalence and risk factors of HCV infection in Rwanda. A total of 324 patients attending Rwanda Military Hospital were randomly selected and a ... ...

    Abstract In Rwanda, the prevalence of viral hepatitis (HCV) is poorly understood. The current study investigated the prevalence and risk factors of HCV infection in Rwanda. A total of 324 patients attending Rwanda Military Hospital were randomly selected and a questionnaire was administered to determine the risk factors. Blood was collected and screened for anti-HCV antibodies and seropositive samples were subjected to polymerase chain reaction method. Hematology abnormalities in the HCV infected patients were also investigated. Anti-HCV antibody and active HCV infection were found in 16.0% and 9.6% of total participants, respectively. Prevalence was highest (28.4%; 19/67) among participants above 55 years and least (2.4%; 3/123) among younger participants (18-35 years). There was a significant (
    MeSH term(s) Adolescent ; Adult ; Demography ; Female ; Hepacivirus/physiology ; Hepatitis C/blood ; Hepatitis C/epidemiology ; Hepatitis C/virology ; Hepatitis C Antibodies/blood ; Hospitals, Military/statistics & numerical data ; Humans ; Male ; Marital Status ; Middle Aged ; Prevalence ; RNA, Viral/blood ; RNA, Viral/genetics ; Residence Characteristics ; Risk Factors ; Rwanda/epidemiology ; Young Adult
    Chemical Substances Hepatitis C Antibodies ; RNA, Viral
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2698540-8
    ISSN 2314-6141 ; 2314-6133
    ISSN (online) 2314-6141
    ISSN 2314-6133
    DOI 10.1155/2017/5841272
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58.

    Rutanga, Jean Pierre / de Block, Tessa / Cuypers, Wim L / Cafmeyer, Josephine / Peeters, Marjan / Umumararungu, Esperance / Ngabonziza, Jean Claude S / Rucogoza, Aniceth / Vandenberg, Olivier / Martiny, Delphine / Dusabe, Angélique / Nkubana, Théoneste / Dougan, Gordon / Muvunyi, Claude Mambo / Mwikarago, Ivan Emil / Jacobs, Jan / Deborggraeve, Stijn / Van Puyvelde, Sandra

    PLoS neglected tropical diseases

    2023  Volume 17, Issue 6, Page(s) e0011285

    Abstract: Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. ...

    Abstract Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and East sub-Saharan Africa. The situation in Rwanda is currently unknown and therefore to reveal the genetic diversity and AMR of S. Typhi in Rwanda, 25 historical (1984-1985) and 26 recent (2010-2018) isolates from Rwanda were analysed using whole genome sequencing (WGS). WGS was locally implemented using Illumina MiniSeq and web-based analysis tools, thereafter complemented with bioinformatic approaches for more in-depth analyses. Whereas historical S. Typhi isolates were found to be fully susceptible to antimicrobials and show a diversity of genotypes, i.e 2.2.2, 2.5, 3.3.1 and 4.1; the recent isolates showed high AMR rates and were predominantly associated with genotype 4.3.1.2 (H58, 22/26; 84,6%), possibly resulting from a single introduction in Rwanda from South Asia before 2010. We identified practical challenges for the use of WGS in endemic regions, including a high cost for shipment of molecular reagents and lack of high-end computational infrastructure for the analyses, but also identified WGS to be feasible in the studied setting and giving opportunity for synergy with other programs.
    MeSH term(s) Humans ; Salmonella typhi/genetics ; Haplotypes ; Anti-Bacterial Agents/therapeutic use ; Rwanda ; Typhoid Fever/epidemiology ; Whole Genome Sequencing ; Microbial Sensitivity Tests
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-06-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2429704-5
    ISSN 1935-2735 ; 1935-2735
    ISSN (online) 1935-2735
    ISSN 1935-2735
    DOI 10.1371/journal.pntd.0011285
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.

    Butera, Yvan / Mukantwari, Enatha / Artesi, Maria / Umuringa, Jeanne d'arc / O'Toole, Áine Niamh / Hill, Verity / Rooke, Stefan / Hong, Samuel Leandro / Dellicour, Simon / Majyambere, Onesphore / Bontems, Sebastien / Boujemla, Bouchra / Quick, Josh / Resende, Paola Cristina / Loman, Nick / Umumararungu, Esperance / Kabanda, Alice / Murindahabi, Marylin Milumbu / Tuyisenge, Patrick /
    Gashegu, Misbah / Rwabihama, Jean Paul / Sindayiheba, Reuben / Gikic, Djordje / Souopgui, Jacob / Ndifon, Wilfred / Rutayisire, Robert / Gatare, Swaibu / Mpunga, Tharcisse / Ngamije, Daniel / Bours, Vincent / Rambaut, Andrew / Nsanzimana, Sabin / Baele, Guy / Durkin, Keith / Mutesa, Leon / Rujeni, Nadine

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 5705

    Abstract: COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift ...

    Abstract COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.
    MeSH term(s) Adult ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Epidemiological Monitoring ; Female ; Genome, Viral/genetics ; Humans ; Male ; Phylogeny ; Phylogeography ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Rwanda/epidemiology ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/pathogenicity ; Travel-Related Illness ; Whole Genome Sequencing
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2021-09-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-25985-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics

    Butera, Yvan / Mukantwari, Enatha / Artesi, Maria / Umuringa, Jeanne D'Arc / O'Toole, Aine Niamh / Hill, Verity / Rooke, Stefan / Hong, Samuel Leandro / Dellicour, Simon / Majyambere, Onesphore / Bontems, Sebastien / Boujemla, Bouchra / Quick, Josh / Resende, Paola Cristina / Loman, Nicholas James / Umumararungu, Esperance / Kabanda, Alice / Murindahabi, Marylin Milumbu / Tuyisenge, Patrick /
    Gashegu, Misbah / Rwabihama, Jean Paul / Sindayiheba, Reuben / Gikic, Djordje / Souopgui, Jacob / Ndifon, Wilfred / Rutayisire, Robert / Gatare, Swaibu / Mpunga, Tharcisse / Ngamije, Daniel / Bours, Vincent / Rambaut, Andrew / Nsanzimana, Sabin / Baele, Guy / Durkin, Keith / Mutesa, Leon / Rujeni, Nadine

    medRxiv

    Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 19 (COVID-19), is a single-stranded positive-sense ribonucleic acid (RNA) virus that typically undergoes one to two single nucleotide mutations per ... ...

    Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 19 (COVID-19), is a single-stranded positive-sense ribonucleic acid (RNA) virus that typically undergoes one to two single nucleotide mutations per month. COVID-19 continues to spread globally, with case fatality and test positivity rates often linked to locally circulating strains of SARS-CoV-2. Furthermore, mutations in this virus, in particular those occurring in the spike protein (involved in the virus binding to the host epithelial cells) have potential implications in current vaccination efforts. In Rwanda, more than twenty thousand cases have been confirmed as of March 14th 2021, with a case fatality rate of 1.4% and test positivity rate of 2.3% while the recovery rate is at 91.9%. Rwanda started its genomic surveillance efforts, taking advantage of pre-existing research projects and partnerships, to ensure early detection of SARS-CoV-2 variants and to potentially contain the spread of variants of concern (VOC). As a result of this initiative, we here present 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in the country from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the newly emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the VOCs, B.1.1.7 and B.1.351, among incoming travelers tested at Kigali International Airport. We also discuss the potential impact of COVID-19 control measures established in the country to control the spread of the virus. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations during the time frame of interest. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences are currently available or that no longer report positive cases. Our results point to the importance of systematically screening all incoming travelers, regardless of the origin of their travels as well as regional considerations for durable response to COVID-19.
    Keywords covid19
    Language English
    Publishing date 2021-04-07
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.04.02.21254839
    Database COVID19

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