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  1. Article ; Online: Serious fungal diseases in Democratic Republic of Congo - Incidence and prevalence estimates.

    Kamwiziku, Guyguy K / Makangara, Jean-Claude C / Orefuwa, Emma / Denning, David W

    Mycoses

    2021  Volume 64, Issue 10, Page(s) 1159–1169

    Abstract: A literature review was conducted to assess the burden of serious fungal infections in the Democratic Republic of the Congo (DRC) (population 95,326,000). English and French publications were listed and analysed using PubMed/Medline, Google Scholar and ... ...

    Abstract A literature review was conducted to assess the burden of serious fungal infections in the Democratic Republic of the Congo (DRC) (population 95,326,000). English and French publications were listed and analysed using PubMed/Medline, Google Scholar and the African Journals database. Publication dates spanning 1943-2020 were included in the scope of the review. From the analysis of published articles, we estimate a total of about 5,177,000 people (5.4%) suffer from serious fungal infections in the DRC annually. The incidence of cryptococcal meningitis, Pneumocystis jirovecii pneumonia in adults and invasive aspergillosis in AIDS patients was estimated at 6168, 2800 and 380 cases per year. Oral and oesophageal candidiasis represent 50,470 and 28,800 HIV-infected patients respectively. Chronic pulmonary aspergillosis post-tuberculosis incidence and prevalence was estimated to be 54,700. Fungal asthma (allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitization) probably has a prevalence of 88,800 and 117,200. The estimated prevalence of recurrent vulvovaginal candidiasis and tinea capitis is 1,202,640 and 3,551,900 respectively.Further work is required to provide additional studies on opportunistic infections for improving diagnosis and the implementation of a national surveillance programme of fungal disease in the DRC.
    MeSH term(s) AIDS-Related Opportunistic Infections/epidemiology ; Adult ; Aspergillosis/epidemiology ; Asthma/epidemiology ; Asthma/microbiology ; Candidiasis/epidemiology ; Cost of Illness ; Democratic Republic of the Congo/epidemiology ; Fungi ; Humans ; Incidence ; Mycoses/epidemiology ; Prevalence
    Language English
    Publishing date 2021-06-25
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 392487-7
    ISSN 1439-0507 ; 0933-7407
    ISSN (online) 1439-0507
    ISSN 0933-7407
    DOI 10.1111/myc.13339
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study.

    Shaw, Alexander G / Mampuela, Tresor Kabeya / Lofiko, Emmanuel Lokilo / Pratt, Catherine / Troman, Catherine / Bujaki, Erika / O'Toole, Áine / Akello, Joyce Odeke / Aziza, Adrienne Amuri / Lusamaki, Eddy Kinganda / Makangara, Jean Claude / Akonga, Marceline / Lay, Yvonne / Nsunda, Bibiche / White, Bailey / Jorgensen, David / Pukuta, Elizabeth / Riziki, Yogolelo / Rankin, Kathleen E /
    Rambaut, Andrew / Ahuka-Mundeke, Steve / Muyembe, Jean-Jacques / Martin, Javier / Grassly, Nicholas C / Mbala-Kingebeni, Placide

    Nature microbiology

    2023  Volume 8, Issue 9, Page(s) 1634–1640

    Abstract: Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a ... ...

    Abstract Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.
    MeSH term(s) Poliovirus/genetics ; Nanopore Sequencing ; Polymerase Chain Reaction ; Dansyl Compounds
    Chemical Substances dimethylaminonaphthalene-5-sulfonaminoethylmethylamine (74686-82-1) ; Dansyl Compounds
    Language English
    Publishing date 2023-08-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01453-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. 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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  4. 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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  5. 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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  6. 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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