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  1. Article ; Online: Vaccine Induced Herd Immunity for Control of Respiratory Syncytial Virus Disease in a Low-Income Country Setting.

    Kinyanjui, Timothy M / House, Thomas A / Kiti, Moses C / Cane, Patricia A / Nokes, David J / Medley, Graham F

    PloS one

    2015  Volume 10, Issue 9, Page(s) e0138018

    Abstract: Background: Respiratory syncytial virus (RSV) is globally ubiquitous, and infection during the first six months of life is a major risk for severe disease and hospital admission; consequently RSV is the most important viral cause of respiratory ... ...

    Abstract Background: Respiratory syncytial virus (RSV) is globally ubiquitous, and infection during the first six months of life is a major risk for severe disease and hospital admission; consequently RSV is the most important viral cause of respiratory morbidity and mortality in young children. Development of vaccines for young infants is complicated by the presence of maternal antibodies and immunological immaturity, but vaccines targeted at older children avoid these problems. Vaccine development for young infants has been unsuccessful, but this is not the case for older children (> 6 m). Would vaccinating older children have a significant public health impact? We developed a mathematical model to explore the benefits of a vaccine against RSV.
    Methods and findings: We have used a deterministic age structured model capturing the key epidemiological characteristics of RSV and performed a statistical maximum-likelihood fit to age-specific hospitalization data from a developing country setting. To explore the effects of vaccination under different mixing assumptions, we included two versions of contact matrices: one from a social contact diary study, and the second a synthesised construction based on demographic data. Vaccination is assumed to elicit an immune response equivalent to primary infection. Our results show that immunisation of young children (5-10 m) is likely to be a highly effective method of protection of infants (<6 m) against hospitalisation. The majority benefit is derived from indirect protection (herd immunity). A full sensitivity and uncertainty analysis using Latin Hypercube Sampling of the parameter space shows that our results are robust to model structure and model parameters.
    Conclusions: This result suggests that vaccinating older infants and children against RSV can have a major public health benefit.
    MeSH term(s) Adolescent ; Adult ; Age Factors ; Aged ; Child ; Child, Preschool ; Computer Simulation ; Hospitalization ; Humans ; Immunity, Herd ; Infant ; Kenya/epidemiology ; Middle Aged ; Models, Biological ; Models, Statistical ; Poverty ; Respiratory Syncytial Virus Infections/epidemiology ; Respiratory Syncytial Virus Infections/immunology ; Respiratory Syncytial Virus Infections/prevention & control ; Respiratory Syncytial Virus Vaccines/immunology ; Respiratory Syncytial Virus Vaccines/therapeutic use ; Respiratory Syncytial Viruses/immunology ; Vaccination ; Young Adult
    Chemical Substances Respiratory Syncytial Virus Vaccines
    Keywords covid19
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0138018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020–2021

    Morobe, John Mwita / Pool, Brigitte / Marie, Lina / Didon, Dwayne / Lambisia, Arnold W. / Makori, Timothy / Mohammed, Khadija Said / de Laurent, Zaydah R. / Ndwiga, Leonard / Mburu, Maureen W. / Moraa, Edidah / Murunga, Nickson / Musyoki, Jennifer / Mwacharo, Jedida / Nyamako, Lydia / Riako, Debra / Ephnatus, Pariken / Gambo, Faith / Naimani, Josephine /
    Namulondo, Joyce / Tembo, Susan Zimba / Ogendi, Edwin / Balde, Thierno / Dratibi, Fred Athanasius / Yahaya, Ali Ahmed / Gumede, Nicksy / Achilla, Rachel A. / Borus, Peter K. / Wanjohi, Dorcas W. / Tessema, Sofonias K. / Mwangangi, Joseph / Bejon, Philip / Nokes, David J. / Ochola-Oyier, Lynette Isabella / Githinji, George / Biscornet, Leon / Agoti, Charles N.

    Viruses. 2022 June 16, v. 14, no. 6

    2022  

    Abstract: Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of ... ...

    Abstract Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; genome ; genomics ; Europe ; Indian Ocean ; Seychelles
    Language English
    Dates of publication 2022-0616
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14061318
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Social Contact Patterns and Implications for Infectious Disease Transmission: A Systematic Review and Meta-Analysis of Contact Surveys.

    Mousa, Andria / Winskill, Peter / Watson, Oliver J / Ratmann, Oliver / Monod, Mélodie / Ajelli, Marco / Diallo, Aldiouma / Dodd, Peter J / Grijalva, Carlos G / Kiti, Moses Chapa / Krishnan, Anand / Kumar, Rakesh / Kumar, Supriya / Kwok, Kin On / Lanata, Claudio F / Le Polain de Waroux, Olivier / Leung, Kathy / Mahikul, Wiriya / Melegaro, Alessia /
    Morrow, Carl D / Mossong, Joël / Neal, Eleanor Fg / Nokes, David J / Pan-Ngum, Wirichada / Potter, Gail E / Russell, Fiona M / Saha, Siddhartha / Sugimoto, Jonathan D / Wei, Wan In / Wood, Robin R / Wu, Joseph T / Zhang, Juanjuan / Walker, Patrick Gt / Whittaker, Charles

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of ... ...

    Abstract Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focussed on high-income settings.
    Methods: Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys we explored how contact characteristics (number, location, duration and whether physical) vary across income settings.
    Results: Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age-groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, but low-income settings were characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income-strata on the frequency, duration and type of contacts individuals made.
    Conclusions: These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens, as well as the effectiveness of different non-pharmaceutical interventions.
    Funding: This work is primarily being funded by joint Centre funding from the UK Medical Research Council and DFID (MR/R015600/1).
    Language English
    Publishing date 2021-06-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.06.10.21258720
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Influenza activity in Kenya, 2007-2013: timing, association with climatic factors, and implications for vaccination campaigns.

    Emukule, Gideon O / Mott, Joshua A / Spreeuwenberg, Peter / Viboud, Cecile / Commanday, Alexander / Muthoka, Philip / Munywoki, Patrick K / Nokes, David J / van der Velden, Koos / Paget, John W

    Influenza and other respiratory viruses

    2016  Volume 10, Issue 5, Page(s) 375–385

    Abstract: Background: Information on the timing of influenza circulation remains scarce in Tropical regions of Africa.: Objectives: We assessed the relationship between influenza activity and several meteorological factors (temperature, specific humidity, ... ...

    Abstract Background: Information on the timing of influenza circulation remains scarce in Tropical regions of Africa.
    Objectives: We assessed the relationship between influenza activity and several meteorological factors (temperature, specific humidity, precipitation) and characterized the timing of influenza circulation and its implications to vaccination strategies in Kenya.
    Methods: We analyzed virologically confirmed influenza data for outpatient influenza-like illness (ILI), hospitalized for severe acute respiratory infections (SARI), and cases of severe pneumonia over the period 2007-2013. Using logistic and negative binomial regression methods, we assessed the independent association between climatic variables (lagged up to 4 weeks) and influenza activity.
    Results: There were multiple influenza epidemics occurring each year and lasting a median duration of 2-4 months. On average, there were two epidemics occurring each year in most of the regions in Kenya, with the first epidemic occurring between the months of February and March and the second one between July and November. Specific humidity was independently and negatively associated with influenza activity. Combinations of low temperature (<18°C) and low specific humidity (<11 g/kg) were significantly associated with increased influenza activity.
    Conclusions: Our study broadens understanding of the relationships between seasonal influenza activity and meteorological factors in the Kenyan context. While rainfall is frequently thought to be associated with influenza circulation in the tropics, the present findings suggest low humidity is more important in Kenya. If annual vaccination were a component of a vaccination strategy in Kenya, the months of April to June are proposed as optimal for associated campaigns.
    MeSH term(s) Child ; Child, Preschool ; Epidemics ; Female ; Humans ; Humidity ; Immunization Programs/standards ; Influenza A virus/isolation & purification ; Influenza Vaccines ; Influenza, Human/epidemiology ; Influenza, Human/prevention & control ; Influenza, Human/virology ; Kenya/epidemiology ; Male ; Meteorological Concepts ; Seasons ; Temperature
    Chemical Substances Influenza Vaccines
    Language English
    Publishing date 2016-05-27
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 2274538-5
    ISSN 1750-2659 ; 1750-2640
    ISSN (online) 1750-2659
    ISSN 1750-2640
    DOI 10.1111/irv.12393
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021.

    Morobe, John Mwita / Pool, Brigitte / Marie, Lina / Didon, Dwayne / Lambisia, Arnold W / Makori, Timothy / Mohammed, Khadija Said / de Laurent, Zaydah R / Ndwiga, Leonard / Mburu, Maureen W / Moraa, Edidah / Murunga, Nickson / Musyoki, Jennifer / Mwacharo, Jedida / Nyamako, Lydia / Riako, Debra / Ephnatus, Pariken / Gambo, Faith / Naimani, Josephine /
    Namulondo, Joyce / Tembo, Susan Zimba / Ogendi, Edwin / Balde, Thierno / Dratibi, Fred Athanasius / Yahaya, Ali Ahmed / Gumede, Nicksy / Achilla, Rachel A / Borus, Peter K / Wanjohi, Dorcas W / Tessema, Sofonias K / Mwangangi, Joseph / Bejon, Philip / Nokes, David J / Ochola-Oyier, Lynette Isabella / Githinji, George / Biscornet, Leon / Agoti, Charles N

    Viruses

    2022  Volume 14, Issue 6

    Abstract: Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of ... ...

    Abstract Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.
    MeSH term(s) COVID-19/epidemiology ; Genomics ; Humans ; SARS-CoV-2/genetics ; Seychelles/epidemiology
    Language English
    Publishing date 2022-06-16
    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/v14061318
    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 / 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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