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  1. Article: Rift Valley Fever Virus, Japanese Encephalitis Virus, and African Swine Fever Virus: Three Transboundary, Vector-Borne, Veterinary Biothreats With Diverse Surveillance, and Response Capacity Needs.

    Kading, Rebekah C / Abworo, Edward O / Hamer, Gabriel L

    Frontiers in veterinary science

    2019  Volume 6, Page(s) 458

    Abstract: Early detection of emerging foreign animal diseases is critical to pathogen surveillance and control programs. Rift valley fever virus (RVFV), Japanese encephalitis virus (JEV), and African swine fever virus (ASFV) represent three taxonomically and ... ...

    Abstract Early detection of emerging foreign animal diseases is critical to pathogen surveillance and control programs. Rift valley fever virus (RVFV), Japanese encephalitis virus (JEV), and African swine fever virus (ASFV) represent three taxonomically and ecologically diverse vector-borne viruses with the potential to be introduced to the United States. To promote preparedness for such an event, we reviewed the current surveillance strategies and diagnostic tools in practice around the world for these emerging viruses, and summarized key points pertaining to the availability of existing guidelines and strategic approaches for early detection, surveillance, and disease management activities. We compare and contrast the surveillance and management approaches of these three diverse agents of disease as case studies to emphasize the importance of the ecological context and biology of vectors and vertebrate hosts. The information presented in this review will inform stakeholders of the current state of surveillance approaches against these transboundary foreign animal disease which threaten the United States.
    Language English
    Publishing date 2019-12-13
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2019.00458
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

    Amimo, Joshua O / Machuka, Eunice M / Abworo, Edward O / Vlasova, Anastasia N / Pelle, Roger

    Viruses. 2020 Nov. 05, v. 12, no. 11

    2020  

    Abstract: Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic ...

    Abstract Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.
    Keywords Mamastrovirus ; Rotavirus ; amino acid sequences ; animal viruses ; coat proteins ; epitopes ; farms ; gastroenteritis ; genetic variation ; genome ; genotype ; human diseases ; livestock and meat industry ; molecular epidemiology ; nucleotide sequences ; piglets ; prediction ; sequence analysis ; subunit vaccines ; Kenya ; Uganda
    Language English
    Dates of publication 2020-1105
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v12111262
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms.

    Amimo, Joshua O / Machuka, Eunice M / Abworo, Edward O / Vlasova, Anastasia N / Pelle, Roger

    Viruses

    2020  Volume 12, Issue 11

    Abstract: Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic ...

    Abstract Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus
    MeSH term(s) Animals ; Astroviridae Infections/epidemiology ; Astroviridae Infections/veterinary ; Farms ; Feces/virology ; Genetic Variation ; Genome, Viral ; Genotype ; Kenya/epidemiology ; Livestock/virology ; Mamastrovirus/genetics ; Phylogeny ; Sequence Analysis ; Swine ; Swine Diseases/epidemiology ; Swine Diseases/virology ; Uganda/epidemiology ; Whole Genome Sequencing
    Language English
    Publishing date 2020-11-05
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v12111262
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic.

    Nasimiyu, Carolyne / Matoke-Muhia, Damaris / Rono, Gilbert K / Osoro, Eric / Obado, Daniel O / Mwangi, J Milkah / Mwikwabe, Nicholas / Thiong'o, Kelvin / Dawa, Jeanette / Ngere, Isaac / Gachohi, John / Kariuki, Samuel / Amukoye, Evans / Mureithi, Marianne / Ngere, Philip / Amoth, Patrick / Were, Ian / Makayotto, Lyndah / Nene, Vishvanath /
    Abworo, Edward O / Njenga, M Kariuki / Seifert, Stephanie N / Oyola, Samuel O

    medRxiv : the preprint server for health sciences

    2022  

    Abstract: Background: Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression.: Methods: SARS-CoV-2 surveillance and testing data were obtained from ... ...

    Abstract Background: Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression.
    Methods: SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens.
    Results: Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of
    Conclusions: The emergence of
    Language English
    Publishing date 2022-02-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2022.02.28.22271467
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

    Nasimiyu, Carolyne / Matoke-Muhia, Damaris / Rono, Gilbert K. / Osoro, Eric / Obado, Daniel O. / Mwanga, J. Milkah / Mwikwabe, Nicholas / Thiong'o, Kelvin / Dawa, Jeanette / Ngere, Isaac / Gachohi, John / Kariuki, Samuel / Amukoye, Evans / Mureithi, Marianne / Ngere, Philip / Amoth, Patrick / Were, Ian / Makayotto, Lyndah / Nene, Vishvanath /
    Abworo, Edward O. / Njenga, M. Kariuki / Seifert, Stephanie N. / Oyola, Samuel O.

    medRxiv

    Abstract: Background. Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. Methods. SARS-CoV-2 surveillance and testing data were obtained from the ... ...

    Abstract Background. Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. Methods. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Results. Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. Conclusions. The emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.
    Keywords covid19
    Language English
    Publishing date 2022-02-28
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2022.02.28.22271467
    Database COVID19

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  6. Article ; Online: Preliminary efficacy investigations of oral fipronil against Anopheles arabiensis when administered to Zebu cattle (Bos indicus) under field conditions

    Poché, R.M. / Githaka, Naftaly W. / Gool, F. van / Kading, R.C. / Hartman, D. / Polyakova, L. / Abworo, Edward O. / Nene, Vishvanath / Lozano-Fuentes, S.

    Acta Tropica

    2017  

    Abstract: Globally, malaria remains one of the most important vector-borne diseases despite the extensive use of vector control, including indoor residual spraying (IRS) and insecticide-treated nets (ITNs). These control methods target endophagic vectors, whereas ... ...

    Abstract Globally, malaria remains one of the most important vector-borne diseases despite the extensive use of vector control, including indoor residual spraying (IRS) and insecticide-treated nets (ITNs). These control methods target endophagic vectors, whereas some malaria vectors, such as Anopheles arabiensis, preferentially feed outdoors on cattle, making it a complicated vector to control using conventional strategies. Our study evaluated whether treating cattle with a capsule containing the active ingredient (AI) fipronil could reduce vector density and sporozoite rates, and alter blood feeding behavior, when applied in a small-scale field study. A pilot field study was carried out in the Samia District, Western Kenya, from May to July 2015. Four plots, each comprised of 50 huts used for sleeping, were randomly designated to serve as control or treatment. A week before cattle treatment, baseline mosquito collections were performed inside the houses using mechanical aspirators. Animals in the treatment (and buffer) were administered a single oral application of fipronil at ∼0.5 mg/kg of body weight. Indoor mosquito collections were performed once a week for four weeks following treatment. Female mosquitoes were first identified morphologically to species complex, followed by PCR-based methods to obtain species identity, sporozoite presence, and the host source of the blood meal. All three species of anophelines found in the study area (An. gambiae s.s., An. arabiensis, An. funestus s.s.) were actively transmitting Plasmodium falciparumduring the study period. The indoor resting density of An. arabiensis was significantly reduced in treatment plot one at three weeks post-treatment (T1) (efficacy = 89%; T1 density = 0.08, 95% credibility intervals [0.05, 0.10]; control plot density = 0.78 [0.22, 0.29]) and at four weeks post-treatment (efficacy = 64%; T1 density = 0.16 [0.08, 0.14]; control plot density = 0.48 [0.17, 0.22]). The reduction of An. arabiensis mosquitoes captured in the treatment plot two was higher: zero ...
    Keywords animal health ; cattle ; health
    Language English
    Publishing date 2017-08-02T09:29:30Z
    Publisher Elsevier
    Publishing country fr
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text 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

    Full text online

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