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  1. Article ; Online: Integrating interferon-gamma release assay testing into provision of tuberculosis preventive therapy is feasible in a tuberculosis high burden resource-limited setting: A mixed methods study.

    Muchuro, Simon / Makabayi-Mugabe, Rita / Musaazi, Joseph / Mayito, Jonathan / Zawedde-Muyanja, Stella / Nakawooya, Mabel / Tugumisirize, Didas / Semanda, Patrick / Wandiga, Steve / Nabada-Ndidde, Susan / Nkolo, Abel / Turyahabwe, Stavia

    PLOS global public health

    2022  Volume 2, Issue 7, Page(s) e0000197

    Abstract: The World Health Organization recommends the scale-up of tuberculosis preventive therapy (TPT) for persons at risk of developing active tuberculosis (TB) as a key component to end the global TB epidemic. We sought to determine the feasibility of ... ...

    Abstract The World Health Organization recommends the scale-up of tuberculosis preventive therapy (TPT) for persons at risk of developing active tuberculosis (TB) as a key component to end the global TB epidemic. We sought to determine the feasibility of integrating testing for latent TB infection (LTBI) using interferon-gamma release assays (IGRAs) into the provision of TPT in a resource-limited high TB burden setting. We conducted a parallel convergent mixed methods study at four tertiary referral hospitals. We abstracted details of patients with bacteriologically confirmed pulmonary tuberculosis (PBC TB). We line-listed household contacts (HHCs) of these patients and carried out home visits where we collected demographic data from HHCs, and tested them for both HIV and LTBI. We performed multi-level Poisson regression with robust standard errors to determine the associations between the presence of LTBI and characteristics of HHCs. Qualitative data was collected from health workers and analyzed using inductive thematic analysis. From February to December 2020 we identified 355 HHCs of 86 index TB patients. Among these HHCs, uptake for the IGRA test was 352/355 (99%) while acceptability was 337/352 (95.7%). Of the 352 HHCs that were tested with IGRA, the median age was 18 years (IQR 10-32), 191 (54%) were female and 11 (3%) were HIV positive. A total of 115/352 (32.7%) had a positive IGRA result. Among HHCs who tested negative on IGRA at the initial visit, 146 were retested after 9 months and 5 (3.4%) of these tested positive for LTBI. At multivariable analysis, being aged ≥ 45 years [PR 2.28 (95% CI 1.02, 5.08)], being employed as a casual labourer [PR 1.38 (95% CI 1.19, 1.61)], spending time with the index TB patient every day [PR 2.14 (95% CI 1.51, 3.04)], being a parent/sibling to the index TB patients [PR 1.39 (95% CI 1.21, 1.60)] and sharing the same room with the index TB patients [PR 1.98 (95% CI 1.52, 2.58)] were associated with LTBI. Implementation challenges included high levels of TB stigma and difficulties in following strict protocols for blood sample storage and transportation. Integrating home-based IGRA testing for LTBI into provision of TB preventive therapy in routine care settings was feasible and resulted in high uptake and acceptability of IGRA tests.
    Language English
    Publishing date 2022-07-06
    Publishing country United States
    Document type Journal Article
    ISSN 2767-3375
    ISSN (online) 2767-3375
    DOI 10.1371/journal.pgph.0000197
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda.

    Bugembe, Daniel Lule / Phan, My V T / Ssewanyana, Isaac / Semanda, Patrick / Nansumba, Hellen / Dhaala, Beatrice / Nabadda, Susan / O'Toole, Áine Niamh / Rambaut, Andrew / Kaleebu, Pontiano / Cotten, Matthew

    Nature microbiology

    2021  Volume 6, Issue 8, Page(s) 1094–1101

    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 ... ...

    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.
    MeSH term(s) Amino Acid Motifs ; COVID-19/epidemiology ; Coronavirus Nucleocapsid Proteins/genetics ; Genetic Variation/genetics ; Genome, Viral/genetics ; Humans ; Phosphoproteins/genetics ; Phylogeny ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Uganda/epidemiology ; Viral Proteins/genetics
    Chemical Substances Coronavirus Nucleocapsid Proteins ; NSP6 protein, SARS-CoV-2 ; ORF8 protein, SARS-CoV-2 ; Phosphoproteins ; Spike Glycoprotein, Coronavirus ; Viral Proteins ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2021-06-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-021-00933-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic

    Lule Bugembe, Daniel / Phan, My V.T. / Ssewanyana, Isaac / Semanda, Patrick / Nansumba, Hellen / Dhaala, Beatrice / Nabadda, Susan / O'Toole, Aine / Rambaut, Andrew / Kaleebu, Pontiano / Cotten, Matthew

    medRxiv

    Abstract: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in March 2020 in Uganda. Recently the epidemic showed a shift of SARS-CoV-2 variant distribution and we report here newly emerging A sub-lineages, A.23 and A.23.1, ... ...

    Abstract The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in March 2020 in Uganda. Recently the epidemic showed a shift of SARS-CoV-2 variant distribution and we report here newly emerging A sub-lineages, A.23 and A.23.1, encoding replacements in the spike protein, nsp6, ORF8 and ORF9, with A.23.1 the major virus lineage now observed in Kampala. Although the clinical impact of the A.23.1 variant is not yet clear it is essential to continue careful monitoring of this variant, as well as rapid assessment of the consequences of the spike protein changes for vaccine efficacy.
    Keywords covid19
    Language English
    Publishing date 2021-02-11
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.02.08.21251393
    Database COVID19

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  4. Article ; Online: Combination of Antibody based rapid diagnostic tests used in an algorithm may improve their performance in SARS CoV-2 diagnosis.

    Kushemererwa, Grace Esther / Kayongo, Ismail / Semanda, Patrick / Nansumba, Hellen / Namulindwa, Christine / Tadeo, Iga / Nyegenye, Wilson / Kiyaga, Charles / Ogwok, Patrick Agwa / Nabadda, Susan / Ssewanyana, Isaac

    medRxiv

    Abstract: Background: Globally response to the SARS-CoV-2 pandemic is highly limited by diagnostic methods. Currently, World Health Organization (WHO) recommends the use of molecular assays for confirmation of SARS-CoV-2 infection which are highly expensive and ... ...

    Abstract Background: Globally response to the SARS-CoV-2 pandemic is highly limited by diagnostic methods. Currently, World Health Organization (WHO) recommends the use of molecular assays for confirmation of SARS-CoV-2 infection which are highly expensive and require specialized laboratory equipment. This is a limitation in mass testing and in low resource settings. SARS CoV-2 IgG/IgM antibody tests have had poor diagnostic performance that do not guarantee their use in diagnostics. In this study we demonstrate a concept of using a combination of RDTs in an algorithm to improve their performance for diagnostics. Method: Eighty six (86) EDTA whole blood samples were collected from SARS-CoV-2 positive cases admitted at Masaka and Mbarara Regional Referral Hospitals in Uganda. These were categorized from day when confirmed positive as follows; category A (0-3 days, 10 samples), category B (4-7 days, 20 samples), Category C (8-17 days, 11 samples) and Category D (18-28 days, 20 samples). Plasma was prepared, transported to the testing laboratory and stored at -200C prior to testing. A total of 13 RDTS were tested following manufacturers instructions. Data was entered in Microsoft Excel exported to STATA for computation of sensitivity and specificity. We computed for all possible combinations of 2 of the 13 RDTS (13C2) that were evaluated in parallel algorithm. Results: The individual sensitives of the RDTs ranged between 74% and 18% and there was a general increasing trend across the categories with days since PCR confirmation. A total of 78 possible combinations of the RDTs to be used in parallel was computated. The combinations of the 2 RDTS improved the sensitivities to 90%. Discussion: We demonstrate that use of RDTs in combinations can improve their overall sensitivity. This approach when used on a wider range of combination of RDTs may yield combinations that can give sensitivities that are of diagnostics relevance in mass testing and low resource setting.
    Keywords covid19
    Language English
    Publishing date 2020-06-29
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.06.26.20140806
    Database COVID19

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  5. Article ; Online: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

    Wilkinson, Eduan / Giovanetti, Marta / Tegally, Houriiyah / San, James E / Lessels, Richard / Cuadros, Diego / Martin, Darren P / Zekri, Abdel-Rahman N / Sangare, Abdoul / Ouedraogo, Abdoul Salam / Sesay, Abdul K / Hammami, Adnene / Amuri, Adrienne A / Sayed, Ahmad / Rebai, Ahmed / Elargoubi, Aida / Keita, Alpha K / Sall, Amadou A / Kone, Amadou /
    Souissi, Amal / Gutierrez, Ana V / Page, Andrew / Lambisia, Arnold / Iranzadeh, Arash / Sylverken, Augustina / Ibrahimi, Azeddine / Kouriba, Bourema / Kleinhans, Bronwyn / Dhaala, Beatrice / Brook, Cara / Williamson, Carolyn / Pratt, Catherine B / Akoua-Koffi, Chantal G / Agoti, Charles / Moranga, Collins M / Nokes, James D / Bridges, Daniel J / Bugembe, Daniel L / Doolabh, Deelan / Ssemwanga, Deogratius / Tshabuila, Derek / Bassirou, Diarra / Amuzu, Dominic S.Y. / Goedhals, Dominique / Maruapula, Dorcas / Ngabana, Edith N / Lusamaki, Eddy / Moraa, Edidah / El Fahime, Elmostafa / Jacob, Emerald / Lokilo, Emmanuel / Mukantwari, Enatha / Belarbi, Essia / Simon-Loriere, Etienne / Anoh, Etile A / Leendertz, Fabian / Ajili, Faida / Wasfi, Fares / Takawira, Faustinos T / Derrar, Fawzi / Bouzid, Feriel / Muyembe, Francisca M / Tanser, Frank / Mbunsu, Gabriel / Thilliez, Gaetan / van Zyl, Gert / Schubert, Grit / Githinji, George / Awandare, Gordon A / Abe, Haruka / Karray, Hela H / Nansumba, Hellen / Elgahzaly, Hesham A / Gumbo, Hlanai / Smeti, Ibtihel / Ayed, Ikhlass B / Gaaloul, Imed / Boubaker, Ilhem B.B. / Gazy, Inbal / Ssewanyana, Isaac / Lekana-Douk, Jean B / Makangara, Jean-Claude C / Tamfum, Jean-Jacques M / Heraud, Jean M / Shaffer, Jeffrey G / Giandhari, Jennifer / Li, Jingjing / Yasuda, Jiro / Mends, Joana Q / Kiconco, Jocelyn / Edwards, Jonathan A / Morobe, John / Nkengasong, John N / Gyapong, John / Kayiwa, John T / Gyamfi, Jones / Farah, Jouali / Ngoi, Joyce M / Namulondo, Joyce / Andeko, Julia C / Lutwama, Julius J / O Grady, Justin / Tumedi, Kefenstse A / Said, Khadija / Hae-Young, Kim / Duedu, Kwabena O / Belyamani, Lahcen / Singh, Lavanya / Martins, Leonardo de O. / Mine, Madisa / el Hefnawi, Mahmoud / Aouni, Mahjoub / Mastouri, Maha / Matsheka, Maitshwarelo I / Kebabonye, Malebogo / Turki, Manel / Nyaga, Martin / Damaris, Matoke / Cotten, Matthew / Mburu, Maureen W / Mpina, Maximillian / Wiley, Michael R / Ali, Mohamed A / Khalifa, Mohamed K / Seadawy, Mohamed G / Ouadghiri, Mouna / Mwenda, Mulenga / Allam, Mushal / Phan, My V.T. / Abid, Nabil / Touil, Nadia / Kharrat, Najla / Ismael, Nalia / Mabunda, Nedio / Hsiao, Nei-yuan / Silochi, Nelson / Saasa, Ngonda / Mulder, Nicola / Combe, Patrice / Semanda, Patrick / Oluniyi, Paul E / Arnaldo, Paulo / Quashie, Peter K / Ayivor-Djanie, Reuben / Bester, Philip A / Dussart, Philippe / Mbala, Placide K / Kaleebu, Pontiano / Njouom, Richard / Gorman, Richmond / Kingsley, Robert A / Carr, Rosina A.A. / Gargouri, Saba / Masmoudi, Saber / Kassim, Samar / Trabelsi, Sameh / Kammoun, Sami / Lemriss, Sanaa / Agwa, Sara H / Calvignac-Spencer, Sebastien / Doumbia, Seydou / Madinda, Sheila M / Aryeetey, Sherihane / Ahmed, Shymaa S / Moyo, Sikhulile / Gaseitsiwe, Simani / Simulundu, Edgar / Lekana-Douki, Sonia / Ouangraoua, Soumeya / Mundeke, Steve A / Panji, Sumir / Pillay, Sureshnee / Engelbrecht, Susan / Nabadda, Susan / Behillil, Sylvie / van der Werf, Sylvie / Aanniz, Tarik / Mashe, Tapfumanei / Mohale, Thabo / Le-Viet, Thanh / Schindler, Tobias / Ramphal, Upasana / Ramuth, Magalutcheemee / Fonseca, Vagner / Enouf, Vincent / Roshdy, Wael H / Ampofo, William / Preiser, Wolfgang / Choga, Wonderful T / Bediako, Yaw / Tebeje, Yenew K. / Naidoo, Yeshnee / de Laurent, Zaydah / Tessema, Sofonias K / de Oliveira, Tulio

    medRxiv

    Abstract: The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas ... ...

    Abstract The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, 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 following 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 breeding ground for new variants.
    Keywords covid19
    Language English
    Publishing date 2021-05-13
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.05.12.21257080
    Database COVID19

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  6. Article ; Online: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

    Wilkinson, Eduan / Giovanetti, Marta / Tegally, Houriiyah / San, James E / Lessells, Richard / Cuadros, Diego / Martin, Darren P / Rasmussen, David A / Zekri, Abdel-Rahman N / Sangare, Abdoul K / Ouedraogo, Abdoul-Salam / Sesay, Abdul K / Priscilla, Abechi / Kemi, Adedotun-Sulaiman / Olubusuyi, Adewunmi M / Oluwapelumi, Adeyemi O O / Hammami, Adnène / Amuri, Adrienne A / Sayed, Ahmad /
    Ouma, Ahmed E O / Elargoubi, Aida / Ajayi, Nnennaya A / Victoria, Ajogbasile F / Kazeem, Akano / George, Akpede / Trotter, Alexander J / Yahaya, Ali A / Keita, Alpha K / Diallo, Amadou / Kone, Amadou / Souissi, Amal / Chtourou, Amel / Gutierrez, Ana V / Page, Andrew J / Vinze, Anika / Iranzadeh, Arash / Lambisia, Arnold / Ismail, Arshad / Rosemary, Audu / Sylverken, Augustina / Femi, Ayoade / Ibrahimi, Azeddine / Marycelin, Baba / Oderinde, Bamidele S / Bolajoko, Bankole / Dhaala, Beatrice / Herring, Belinda L / Njanpop-Lafourcade, Berthe-Marie / Kleinhans, Bronwyn / McInnis, Bronwyn / Tegomoh, Bryan / Brook, Cara / Pratt, Catherine B / Scheepers, Cathrine / Akoua-Koffi, Chantal G / Agoti, Charles N / Peyrefitte, Christophe / Daubenberger, Claudia / Morang'a, Collins M / Nokes, D James / Amoako, Daniel G / Bugembe, Daniel L / Park, Danny / Baker, David / Doolabh, Deelan / Ssemwanga, Deogratius / Tshiabuila, Derek / Bassirou, Diarra / Amuzu, Dominic S Y / Goedhals, Dominique / Omuoyo, Donwilliams O / Maruapula, Dorcas / Foster-Nyarko, Ebenezer / Lusamaki, Eddy K / Simulundu, Edgar / Ong'era, Edidah M / Ngabana, Edith N / Shumba, Edwin / El Fahime, Elmostafa / Lokilo, Emmanuel / Mukantwari, Enatha / Philomena, Eromon / Belarbi, Essia / Simon-Loriere, Etienne / Anoh, Etilé A / Leendertz, Fabian / Ajili, Faida / Enoch, Fakayode O / Wasfi, Fares / Abdelmoula, Fatma / Mosha, Fausta S / Takawira, Faustinos T / Derrar, Fawzi / Bouzid, Feriel / Onikepe, Folarin / Adeola, Fowotade / Muyembe, Francisca M / Tanser, Frank / Dratibi, Fred A / Mbunsu, Gabriel K / Thilliez, Gaetan / Kay, Gemma L / Githinji, George / van Zyl, Gert / Awandare, Gordon A / Schubert, Grit / Maphalala, Gugu P / Ranaivoson, Hafaliana C / Lemriss, Hajar / Anise, Happi / Abe, Haruka / Karray, Hela H / Nansumba, Hellen / Elgahzaly, Hesham A / Gumbo, Hlanai / Smeti, Ibtihel / Ayed, Ikhlas B / Odia, Ikponmwosa / Ben Boubaker, Ilhem Boutiba / Gaaloul, Imed / Gazy, Inbal / Mudau, Innocent / Ssewanyana, Isaac / Konstantinus, Iyaloo / Lekana-Douk, Jean B / Makangara, Jean-Claude C / Tamfum, Jean-Jacques M / Heraud, Jean-Michel / Shaffer, Jeffrey G / Giandhari, Jennifer / Li, Jingjing / Yasuda, Jiro / Mends, Joana Q / Kiconco, Jocelyn / Morobe, John M / Gyapong, John O / Okolie, Johnson C / Kayiwa, John T / Edwards, Johnathan A / Gyamfi, Jones / Farah, Jouali / Nakaseegu, Joweria / Ngoi, Joyce M / Namulondo, Joyce / Andeko, Julia C / Lutwama, Julius J / O'Grady, Justin / Siddle, Katherine / Adeyemi, Kayode T / Tumedi, Kefentse A / Said, Khadija M / Hae-Young, Kim / Duedu, Kwabena O / Belyamani, Lahcen / Fki-Berrajah, Lamia / Singh, Lavanya / Martins, Leonardo de O / Tyers, Lynn / Ramuth, Magalutcheemee / Mastouri, Maha / Aouni, Mahjoub / El Hefnawi, Mahmoud / Matsheka, Maitshwarelo I / Kebabonye, Malebogo / Diop, Mamadou / Turki, Manel / Paye, Marietou / Nyaga, Martin M / Mareka, Mathabo / Damaris, Matoke-Muhia / Mburu, Maureen W / Mpina, Maximillian / Nwando, Mba / Owusu, Michael / Wiley, Michael R / Youtchou, Mirabeau T / Ayekaba, Mitoha O / Abouelhoda, Mohamed / Seadawy, Mohamed G / Khalifa, Mohamed K / Sekhele, Mooko / Ouadghiri, Mouna / Diagne, Moussa M / Mwenda, Mulenga / Allam, Mushal / Phan, My V T / Abid, Nabil / Touil, Nadia / Rujeni, Nadine / Kharrat, Najla / Ismael, Nalia / Dia, Ndongo / Mabunda, Nedio / Hsiao, Nei-Yuan / Silochi, Nelson B / Nsenga, Ngoy / Gumede, Nicksy / Mulder, Nicola / Ndodo, Nnaemeka / Razanajatovo, Norosoa H / Iguosadolo, Nosamiefan / Judith, Oguzie / Kingsley, Ojide C / Sylvanus, Okogbenin / Peter, Okokhere / Femi, Oladiji / Idowu, Olawoye / Testimony, Olumade / Chukwuma, Omoruyi E / Ogah, Onwe E / Onwuamah, Chika K / Cyril, Oshomah / Faye, Ousmane / Tomori, Oyewale / Ondoa, Pascale / Combe, Patrice / Semanda, Patrick / Oluniyi, Paul E / Arnaldo, Paulo / Quashie, Peter K / Dussart, Philippe / Bester, Phillip A / Mbala, Placide K / Ayivor-Djanie, Reuben / Njouom, Richard / Phillips, Richard O / Gorman, Richmond / Kingsley, Robert A / Carr, Rosina A A / El Kabbaj, Saâd / Gargouri, Saba / Masmoudi, Saber / Sankhe, Safietou / Lawal, Salako B / Kassim, Samar / Trabelsi, Sameh / Metha, Samar / Kammoun, Sami / Lemriss, Sanaâ / Agwa, Sara H A / Calvignac-Spencer, Sébastien / Schaffner, Stephen F / Doumbia, Seydou / Mandanda, Sheila M / Aryeetey, Sherihane / Ahmed, Shymaa S / Elhamoumi, Siham / Andriamandimby, Soafy / Tope, Sobajo / Lekana-Douki, Sonia / Prosolek, Sophie / Ouangraoua, Soumeya / Mundeke, Steve A / Rudder, Steven / Panji, Sumir / Pillay, Sureshnee / Engelbrecht, Susan / Nabadda, Susan / Behillil, Sylvie / Budiaki, Sylvie L / van der Werf, Sylvie / Mashe, Tapfumanei / Aanniz, Tarik / Mohale, Thabo / Le-Viet, Thanh / Schindler, Tobias / Anyaneji, Ugochukwu J / Chinedu, Ugwu / Ramphal, Upasana / Jessica, Uwanibe / George, Uwem / Fonseca, Vagner / Enouf, Vincent / Gorova, Vivianne / Roshdy, Wael H / Ampofo, William K / Preiser, Wolfgang / Choga, Wonderful T / Bediako, Yaw / Naidoo, Yeshnee / Butera, Yvan / de Laurent, Zaydah R / Sall, Amadou A / Rebai, Ahmed / von Gottberg, Anne / Kouriba, Bourema / Williamson, Carolyn / Bridges, Daniel J / Chikwe, Ihekweazu / Bhiman, Jinal N / Mine, Madisa / Cotten, Matthew / Moyo, Sikhulile / Gaseitsiwe, Simani / Saasa, Ngonda / Sabeti, Pardis C / Kaleebu, Pontiano / Tebeje, Yenew K / Tessema, Sofonias K / Happi, Christian / Nkengasong, John / de Oliveira, Tulio

    Science (New York, N.Y.)

    2021  Volume 374, Issue 6566, Page(s) 423–431

    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 ... ...

    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.
    MeSH term(s) Africa/epidemiology ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Epidemiological Monitoring ; Genetic Variation ; Genomics ; Humans ; Pandemics ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
    Language English
    Publishing date 2021-09-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abj4336
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

    Tegally, Houriiyah / San, James E / Cotten, Matthew / Moir, Monika / Tegomoh, Bryan / Mboowa, Gerald / Martin, Darren P / Baxter, Cheryl / Lambisia, Arnold W / Diallo, Amadou / Amoako, Daniel G / Diagne, Moussa M / Sisay, Abay / Zekri, Abdel-Rahman N / Gueye, Abdou Salam / Sangare, Abdoul K / Ouedraogo, Abdoul-Salam / Sow, Abdourahmane / Musa, Abdualmoniem O /
    Sesay, Abdul K / Abias, Abe G / Elzagheid, Adam I / Lagare, Adamou / Kemi, Adedotun-Sulaiman / Abar, Aden Elmi / Johnson, Adeniji A / Fowotade, Adeola / Oluwapelumi, Adeyemi O / Amuri, Adrienne A / Juru, Agnes / Kandeil, Ahmed / Mostafa, Ahmed / Rebai, Ahmed / Sayed, Ahmed / Kazeem, Akano / Balde, Aladje / Christoffels, Alan / Trotter, Alexander J / Campbell, Allan / Keita, Alpha K / Kone, Amadou / Bouzid, Amal / Souissi, Amal / Agweyu, Ambrose / Naguib, Amel / Gutierrez, Ana V / Nkeshimana, Anatole / Page, Andrew J / Yadouleton, Anges / Vinze, Anika / Happi, Anise N / Chouikha, Anissa / Iranzadeh, Arash / Maharaj, Arisha / Batchi-Bouyou, Armel L / Ismail, Arshad / Sylverken, Augustina A / Goba, Augustine / Femi, Ayoade / Sijuwola, Ayotunde E / Marycelin, Baba / Salako, Babatunde L / Oderinde, Bamidele S / Bolajoko, Bankole / Diarra, Bassirou / Herring, Belinda L / Tsofa, Benjamin / Lekana-Douki, Bernard / Mvula, Bernard / Njanpop-Lafourcade, Berthe-Marie / Marondera, Blessing T / Khaireh, Bouh Abdi / Kouriba, Bourema / Adu, Bright / Pool, Brigitte / McInnis, Bronwyn / Brook, Cara / Williamson, Carolyn / Nduwimana, Cassien / Anscombe, Catherine / Pratt, Catherine B / Scheepers, Cathrine / Akoua-Koffi, Chantal G / Agoti, Charles N / Mapanguy, Chastel M / Loucoubar, Cheikh / Onwuamah, Chika K / Ihekweazu, Chikwe / Malaka, Christian N / Peyrefitte, Christophe / Grace, Chukwa / Omoruyi, Chukwuma E / Rafaï, Clotaire D / Morang'a, Collins M / Erameh, Cyril / Lule, Daniel B / Bridges, Daniel J / Mukadi-Bamuleka, Daniel / Park, Danny / Rasmussen, David A / Baker, David / Nokes, David J / Ssemwanga, Deogratius / Tshiabuila, Derek / Amuzu, Dominic S Y / Goedhals, Dominique / Grant, Donald S / Omuoyo, Donwilliams O / Maruapula, Dorcas / Wanjohi, Dorcas W / Foster-Nyarko, Ebenezer / Lusamaki, Eddy K / Simulundu, Edgar / Ong'era, Edidah M / Ngabana, Edith N / Abworo, Edward O / Otieno, Edward / Shumba, Edwin / Barasa, Edwine / Ahmed, El Bara / Ahmed, Elhadi A / Lokilo, Emmanuel / Mukantwari, Enatha / Philomena, Eromon / Belarbi, Essia / Simon-Loriere, Etienne / Anoh, Etilé A / Manuel, Eusebio / Leendertz, Fabian / Taweh, Fahn M / Wasfi, Fares / Abdelmoula, Fatma / Takawira, Faustinos T / Derrar, Fawzi / Ajogbasile, Fehintola V / Treurnicht, Florette / Onikepe, Folarin / Ntoumi, Francine / Muyembe, Francisca M / Ragomzingba, Frank E Z / Dratibi, Fred A / Iyanu, Fred-Akintunwa / Mbunsu, Gabriel K / Thilliez, Gaetan / Kay, Gemma L / Akpede, George O / van Zyl, Gert U / Awandare, Gordon A / Kpeli, Grace S / Schubert, Grit / Maphalala, Gugu P / Ranaivoson, Hafaliana C / Omunakwe, Hannah E / Onywera, Harris / Abe, Haruka / Karray, Hela / Nansumba, Hellen / Triki, Henda / Kadjo, Herve Albéric Adje / Elgahzaly, Hesham / Gumbo, Hlanai / Mathieu, Hota / Kavunga-Membo, Hugo / Smeti, Ibtihel / Olawoye, Idowu B / Adetifa, Ifedayo M O / Odia, Ikponmwosa / Ben Boubaker, Ilhem Boutiba / Muhammad, Iluoreh Ahmed / Ssewanyana, Isaac / Wurie, Isatta / Konstantinus, Iyaloo S / Halatoko, Jacqueline Wemboo Afiwa / Ayei, James / Sonoo, Janaki / Makangara, Jean-Claude C / Tamfum, Jean-Jacques M / Heraud, Jean-Michel / Shaffer, Jeffrey G / Giandhari, Jennifer / Musyoki, Jennifer / Nkurunziza, Jerome / Uwanibe, Jessica N / Bhiman, Jinal N / Yasuda, Jiro / Morais, Joana / Kiconco, Jocelyn / Sandi, John D / Huddleston, John / Odoom, John K / Morobe, John M / Gyapong, John O / Kayiwa, John T / Okolie, Johnson C / Xavier, Joicymara S / Gyamfi, Jones / Wamala, Joseph F / Bonney, Joseph H K / Nyandwi, Joseph / Everatt, Josie / Nakaseegu, Joweria / Ngoi, Joyce M / Namulondo, Joyce / Oguzie, Judith U / Andeko, Julia C / Lutwama, Julius J / Mogga, Juma J H / O'Grady, Justin / Siddle, Katherine J / Victoir, Kathleen / Adeyemi, Kayode T / Tumedi, Kefentse A / Carvalho, Kevin S / Mohammed, Khadija Said / Dellagi, Koussay / Musonda, Kunda G / Duedu, Kwabena O / Fki-Berrajah, Lamia / Singh, Lavanya / Kepler, Lenora M / Biscornet, Leon / de Oliveira Martins, Leonardo / Chabuka, Lucious / Olubayo, Luicer / Ojok, Lul Deng / Deng, Lul Lojok / Ochola-Oyier, Lynette I / Tyers, Lynn / Mine, Madisa / Ramuth, Magalutcheemee / Mastouri, Maha / ElHefnawi, Mahmoud / Mbanne, Maimouna / Matsheka, Maitshwarelo I / Kebabonye, Malebogo / Diop, Mamadou / Momoh, Mambu / Lima Mendonça, Maria da Luz / Venter, Marietjie / Paye, Marietou F / Faye, Martin / Nyaga, Martin M / Mareka, Mathabo / Damaris, Matoke-Muhia / Mburu, Maureen W / Mpina, Maximillian G / Owusu, Michael / Wiley, Michael R / Tatfeng, Mirabeau Y / Ayekaba, Mitoha Ondo'o / Abouelhoda, Mohamed / Beloufa, Mohamed Amine / Seadawy, Mohamed G / Khalifa, Mohamed K / Matobo, Mooko Marethabile / Kane, Mouhamed / Salou, Mounerou / Mbulawa, Mphaphi B / Mwenda, Mulenga / Allam, Mushal / Phan, My V T / Abid, Nabil / Rujeni, Nadine / Abuzaid, Nadir / Ismael, Nalia / Elguindy, Nancy / Top, Ndeye Marieme / Dia, Ndongo / Mabunda, Nédio / Hsiao, Nei-Yuan / Silochi, Nelson Boricó / Francisco, Ngiambudulu M / Saasa, Ngonda / Bbosa, Nicholas / Murunga, Nickson / Gumede, Nicksy / Wolter, Nicole / Sitharam, Nikita / Ndodo, Nnaemeka / Ajayi, Nnennaya A / Tordo, Noël / Mbhele, Nokuzola / Razanajatovo, Norosoa H / Iguosadolo, Nosamiefan / Mba, Nwando / Kingsley, Ojide C / Sylvanus, Okogbenin / Femi, Oladiji / Adewumi, Olubusuyi M / Testimony, Olumade / Ogunsanya, Olusola A / Fakayode, Oluwatosin / Ogah, Onwe E / Oludayo, Ope-Ewe / Faye, Ousmane / Smith-Lawrence, Pamela / Ondoa, Pascale / Combe, Patrice / Nabisubi, Patricia / Semanda, Patrick / Oluniyi, Paul E / Arnaldo, Paulo / Quashie, Peter Kojo / Okokhere, Peter O / Bejon, Philip / Dussart, Philippe / Bester, Phillip A / Mbala, Placide K / Kaleebu, Pontiano / Abechi, Priscilla / El-Shesheny, Rabeh / Joseph, Rageema / Aziz, Ramy Karam / Essomba, René G / Ayivor-Djanie, Reuben / Njouom, Richard / Phillips, Richard O / Gorman, Richmond / Kingsley, Robert A / Neto Rodrigues, Rosa Maria D E S A / Audu, Rosemary A / Carr, Rosina A A / Gargouri, Saba / Masmoudi, Saber / Bootsma, Sacha / Sankhe, Safietou / Mohamed, Sahra Isse / Femi, Saibu / Mhalla, Salma / Hosch, Salome / Kassim, Samar Kamal / Metha, Samar / Trabelsi, Sameh / Agwa, Sara Hassan / Mwangi, Sarah Wambui / Doumbia, Seydou / Makiala-Mandanda, Sheila / Aryeetey, Sherihane / Ahmed, Shymaa S / Ahmed, Side Mohamed / Elhamoumi, Siham / Moyo, Sikhulile / Lutucuta, Silvia / Gaseitsiwe, Simani / Jalloh, Simbirie / Andriamandimby, Soa Fy / Oguntope, Sobajo / Grayo, Solène / Lekana-Douki, Sonia / Prosolek, Sophie / Ouangraoua, Soumeya / van Wyk, Stephanie / Schaffner, Stephen F / Kanyerezi, Stephen / Ahuka-Mundeke, Steve / Rudder, Steven / Pillay, Sureshnee / Nabadda, Susan / Behillil, Sylvie / Budiaki, Sylvie L / van der Werf, Sylvie / Mashe, Tapfumanei / Mohale, Thabo / Le-Viet, Thanh / Velavan, Thirumalaisamy P / Schindler, Tobias / Maponga, Tongai G / Bedford, Trevor / Anyaneji, Ugochukwu J / Chinedu, Ugwu / Ramphal, Upasana / George, Uwem E / Enouf, Vincent / Nene, Vishvanath / Gorova, Vivianne / Roshdy, Wael H / Karim, Wasim Abdul / Ampofo, William K / Preiser, Wolfgang / Choga, Wonderful T / Ahmed, Yahaya Ali / Ramphal, Yajna / Bediako, Yaw / Naidoo, Yeshnee / Butera, Yvan / de Laurent, Zaydah R / Ouma, Ahmed E O / von Gottberg, Anne / Githinji, George / Moeti, Matshidiso / Tomori, Oyewale / Sabeti, Pardis C / Sall, Amadou A / Oyola, Samuel O / Tebeje, Yenew K / Tessema, Sofonias K / de Oliveira, Tulio / Happi, Christian / Lessells, Richard / Nkengasong, John / Wilkinson, Eduan

    Science (New York, N.Y.)

    2022  Volume 378, Issue 6615, Page(s) eabq5358

    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 ... ...

    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.
    MeSH term(s) Africa/epidemiology ; COVID-19/epidemiology ; COVID-19/virology ; Epidemiological Monitoring ; Genomics ; Humans ; Pandemics ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-10-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abq5358
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

    Tegally, Houriiyah / San, James E. / Cotten, Matthew / Tegomoh, Bryan / Mboowa, Gerald / Martin, Darren P. / Baxter, Cheryl / Moir, Monika / Lambisia, Arnold / Diallo, Amadou / Amoako, Daniel G. / Diagne, Moussa M. / Sisay, Abay / Zekri, Abdel-Rahman N. / Barakat, Abdelhamid / Gueye, Abdou Salam / Sangare, Abdoul K. / Ouedraogo, Abdoul-Salam / SOW, Abdourahmane /
    Musa, Abdualmoniem O. / Sesay, Abdul K. / LAGARE, Adamou / Kemi, Adedotun-Sulaiman / Abar, Aden Elmi / Johnson, Adeniji A. / Fowotade, Adeola / Olubusuyi, Adewumi M. / Oluwapelumi, Adeyemi O. / Amuri, Adrienne A. / Juru, Agnes / Ramadan, Ahmad Mabrouk / Kandeil, Ahmed / Mostafa, Ahmed / Rebai, Ahmed / Sayed, Ahmed / Kazeem, Akano / Balde, Aladje / Christoffels, Alan / Trotter, Alexander J. / Campbell, Allan / KEITA, Alpha Kabinet / Kone, Amadou / Bouzid, Amal / Souissi, Amal / Agweyu, Ambrose / Gutierrez, Ana V. / Page, Andrew J. / Yadouleton, Anges / Vinze, Anika / Happi, Anise N. / Chouikha, Anissa / Iranzadeh, Arash / Maharaj, Arisha / Batchi-Bouyou, Armel Landry / Ismail, Arshad / Sylverken, Augustina / Goba, Augustine / Femi, Ayoade / Sijuwola, Ayotunde Elijah / Ibrahimi, Azeddine / Marycelin, Baba / Salako, Babatunde Lawal / Oderinde, Bamidele S. / Bolajoko, Bankole / Dhaala, Beatrice / Herring, Belinda L. / Tsofa, Benjamin / Mvula, Bernard / Njanpop-Lafourcade, Berthe-Marie / Marondera, Blessing T. / KHAIREH, Bouh Abdi / Kouriba, Bourema / Adu, Bright / Pool, Brigitte / McInnis, Bronwyn / Brook, Cara / Williamson, Carolyn / Anscombe, Catherine / Pratt, Catherine B. / Scheepers, Cathrine / Akoua-Koffi, Chantal G. / Agoti, Charles N. / Loucoubar, Cheikh / Onwuamah, Chika Kingsley / Ihekweazu, Chikwe / MALAKA, Christian Noel / Peyrefitte, Christophe / Omoruyi, Chukwuma Ewean / Rafai, Clotaire Donatien / Morang'a, Collins M. / Nokes, D. James / Lule, Daniel Bugembe / Bridges, Daniel J. / Mukadi-Bamuleka, Daniel / Park, Danny / Baker, David / Doolabh, Deelan / Ssemwanga, Deogratius / Tshiabuila, Derek / Bassirou, Diarra / Amuzu, Dominic S.Y. / Goedhals, Dominique / Grant, Donald S. / Omuoyo, Donwilliams O. / Maruapula, Dorcas / Wanjohi, Dorcas Waruguru / Foster-Nyarko, Ebenezer / Lusamaki, Eddy K. / Simulundu, Edgar / Ong'era, Edidah M. / Ngabana, Edith N. / Abworo, Edward O. / Otieno, Edward / Shumba, Edwin / Barasa, Edwine / AHMED, EL BARA / EL FAHIME, Elmostafa / Lokilo, Emmanuel / Mukantwari, Enatha / Cyril, Erameh / Philomena, Eromon / Belarbi, Essia / Simon-Loriere, Etienne / Anoh, Etile A. / Leendertz, Fabian / Taweh, Fahn M. / Wasfi, Fares / Abdelmoula, Fatma / Takawira, Faustinos T. / Derrar, Fawzi / Ajogbasile, Fehintola V / Treurnicht, Florette / Onikepe, Folarin / Ntoumi, Francine / Muyembe, Francisca M. / NGIAMBUDULU, FRANCISCO / Ragomzingba, Frank Edgard ZONGO / DRATIBI, Fred Athanasius / Iyanu, Fred-Akintunwa / Mbunsu, Gabriel K. / Thilliez, Gaetan / Kay, Gemma L. / Akpede, George O. / Uwem, George E / van Zyl, Gert / Awandare, Gordon A. / Schubert, Grit / Maphalala, Gugu P. / Ranaivoson, Hafaliana C. / Lemriss, Hajar / Omunakwe, Hannah E / Onywera, Harris / Abe, Haruka / KARRAY, HELA / Nansumba, Hellen / Triki, Henda / ADJE KADJO, Herve Alberic / Elgahzaly, Hesham / Gumbo, Hlanai / mathieu, HOTA / Kavunga-Membo, Hugo / Smeti, Ibtihel / Olawoye, Idowu B. / Adetifa, Ifedayo / Odia, Ikponmwosa / Boubaker, Ilhem Boutiba-Ben / Ssewanyana, Isaac / Wurie, Isatta / Konstantinus, Iyaloo S / Halatoko, Jacqueline Wemboo Afiwa / Ayei, James / Sonoo, Janaki / LEKANA-DOUKI, Jean Bernard / Makangara, Jean-Claude C. / Tamfum, Jean-Jacques M. / Heraud, Jean-Michel / Shaffer, Jeffrey G. / Giandhari, Jennifer / Musyoki, Jennifer / Uwanibe, Jessica N. / Bhiman, Jinal N. / Yasuda, Jiro / Morais, Joana / Mends, Joana Q. / Kiconco, Jocelyn / Sandi, John Demby / Huddleston, John / Odoom, John Kofi / Morobe, John M. / Gyapong, John O. / Kayiwa, John T. / Okolie, Johnson C. / Xavier, Joicymara Santos / Gyamfi, Jones / Bonney, Joseph Humphrey Kofi / Nyandwi, Joseph / Everatt, Josie / Farah, Jouali / Nakaseegu, Joweria / Ngoi, Joyce M. / Namulondo, Joyce / Oguzie, Judith U. / Andeko, Julia C. / Lutwama, Julius J. / O'Grady, Justin / Siddle, Katherine J / Victoir, Kathleen / Adeyemi, Kayode T. / Tumedi, Kefentse A. / Carvalho, Kevin Sanders / Mohammed, Khadija Said / Musonda, Kunda G. / Duedu, Kwabena O. / Belyamani, Lahcen / Fki-Berrajah, Lamia / Singh, Lavanya / Biscornet, Leon / de Oliveira Martins, Leonardo / Chabuka, Lucious / Olubayo, Luicer / Deng, Lul Lojok / Ochola-Oyier, Lynette Isabella / Mine, Madisa / Ramuth, Magalutcheemee / Mastouri, Maha / ElHefnawi, Mahmoud / Mbanne, Maimouna / Matsheka, Maitshwarelo I. / Kebabonye, Malebogo / Diop, Mamadou / Momoh, Mambu / da Luz Lima Mendonca, Maria / Venter, Marietjie / Paye, Marietou F / Faye, Martin / Nyaga, Martin M. / Mareka, Mathabo / Damaris, Matoke-Muhia / Mburu, Maureen W. / Mpina, Maximillian / MFOUTOU MAPANGUY, Claujens Chastel / Owusu, Michael / Wiley, Michael R. / Tatfeng, Mirabeau Youtchou / Ayekaba, Mitoha Ondo'o / Abouelhoda, Mohamed / Beloufa, Mohamed Amine / Seadawy, Mohamed G / Khalifa, Mohamed K. / DELLAGI, Mohammed Koussai / Matobo, Mooko Marethabile / Kane, Mouhamed / Ouadghiri, Mouna / Salou, Mounerou / Mbulawa, Mphaphi B. / Saibu, Mudashiru Femi / Mwenda, Mulenga / Phan, My V.T. / Abid, Nabil / Touil, Nadia / Rujeni, Nadine / Ismael, Nalia / Top, Ndeye Marieme / Dia, Ndongo / Mabunda, Nedio / Hsiao, Nei-yuan / Silochi, Nelson Borico / Saasa, Ngonda / Bbosa, Nicholas / Murunga, Nickson / Gumede, Nicksy / Wolter, Nicole / Sitharam, Nikita / Ndodo, Nnaemeka / Ajayi, Nnennaya A. / Tordo, Noel / Mbhele, Nokuzola / Razanajatovo, Norosoa H / Iguosadolo, Nosamiefan / Mba, Nwando / Kingsley, Ojide C. / Sylvanus, Okogbenin / Peter, Okokhere / Femi, Oladiji / Testimony, Olumade / Ogunsanya, Olusola Akinola / Fakayode, Oluwatosin / Ogah, Onwe E. / Faye, Ousmane / Smith-Lawrence, Pamela / Ondoa, Pascale / Combe, Patrice / Nabisubi, Patricia / Semanda, Patrick / Oluniyi, Paul E. / Arnaldo, Paulo / Quashie, Peter Kojo / Bejon, Philip / Dussart, Philippe / Bester, Phillip A. / Mbala, Placide K. / Kaleebu, Pontiano / Abechi, Priscilla / El-Shesheny, Rabeh / Joseph, Rageema / Aziz, Ramy Karam / Essomba, Rene Ghislain / Ayivor-Djanie, Reuben / Njouom, Richard / Phillips, Richard O. / Gorman, Richmond / Kingsley, Robert A. / Audu, Rosemary / Carr, Rosina A.A. / El Kabbaj, Saad / Gargouri, Saba / Masmoudi, Saber / Sankhe, Safietou / Mohamed, Sahra Isse / MHALLA, Salma / Hosch, Salome / Kassim, Samar Kamal / Metha, Samar / Trabelsi, Sameh / Lemriss, Sanaa / Agwa, Sara Hassan / Mwangi, Sarah Wambui / Doumbia, Seydou / Makiala-Mandanda, Sheila / Aryeetey, Sherihane / Ahmed, Shymaa S. / AHMED, SIDI MOHAMED / Elhamoumi, Siham / Moyo, Sikhulile / Lutucuta, Silvia / Gaseitsiwe, Simani / Jalloh, Simbirie / Andriamandimby, Soafy / Oguntope, Sobajo / Grayo, Solene / Lekana-Douki, Sonia / Prosolek, Sophie / Ouangraoua, Soumeya / van Wyk, Stephanie / Schaffner, Stephen F. / Kanyerezi, Stephen / AHUKA-MUNDEKE, Steve / Rudder, Steven / Pillay, Sureshnee / Nabadda, Susan / Behillil, Sylvie / Budiaki, Sylvie L. / van der Werf, Sylvie / Mashe, Tapfumanei / Aanniz, Tarik / Mohale, Thabo / Le-Viet, Thanh / Velavan, Thirumalaisamy P. / Schindler, Tobias / Maponga, Tongai / Bedford, Trevor / Anyaneji, Ugochukwu J. / Chinedu, Ugwu / Ramphal, Upasana / Enouf, Vincent / Nene, Vishvanath / Gorova, Vivianne / Roshdy, Wael H. / Abdul Karim, Wasim / Ampofo, William K. / Preiser, Wolfgang / Choga, Wonderful T. / ALI AHMED, Yahaya ALI / Ramphal, Yajna / Bediako, Yaw / Naidoo, Yeshnee / Butera, Yvan / de Laurent, Zaydah R. / Ouma, Ahmed E.O. / von Gottberg, Anne / Githinji, George / Moeti, Matshidiso / Tomori, Oyewale / Sabeti, Pardis C. / Sall, Amadou A. / Oyola, Samuel O. / Tebeje, Yenew K. / Tessema, Sofonias K. / de Oliveira, Tulio / Happi, Christian / Lessells, Richard / Nkengasong, John / Wilkinson, Eduan

    medRxiv

    Abstract: Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number ...

    Abstract Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.
    Keywords covid19
    Language English
    Publishing date 2022-04-20
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2022.04.17.22273906
    Database COVID19

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